Provides (semi-)alphabets for representing elements in CIGAR strings. More...
Classes | |
class | seqan3::cigar |
The cigar semialphabet pairs a counter with a seqan3::cigar_op letter. More... | |
class | seqan3::cigar_op |
The (extended) cigar operation alphabet of M,D,I,H,N,P,S,X,=. More... | |
Provides (semi-)alphabets for representing elements in CIGAR strings.
CIGAR strings are combinations of count values and CIGAR operations, representing an alignment as a sequence of edit operations. This submodule has two different alphabets. One is the seqan3::cigar_op alphabet, which is a base seqan3::alphabet implementation. This contains all valid symbols contained in CIGAR strings. The other alphabet is the seqan3::cigar alphabet, which is an alphabet tuple. It combines the seqan3::cigar_op alphabet with a count value, such that one can represent an entire CIGAR string with a std::vector of seqan3::cigar values.
The following table outlines the valid characters in the seqan3::cigar_op alphabet.
Letter | Description |
---|---|
M | Alignment match (can be a sequence match or mismatch, used only in basic CIGAR representations) |
I | Insertion to the reference |
D | Deletion from the reference |
N | Skipped region from the reference |
S | Soft clipping (clipped sequences present in SEQ) |
H | Hard clipping (clipped sequences NOT present in SEQ) |
P | Padding (silent deletion from padded reference) |
= | Sequence match |
X | Sequence mismatch |